Awakening
by AdventReign
Summary: What if Shinji were conscious for all those years trapped in Unit 01?


**AWAKENING**

_Beep. Beep. Beep. Ding._

The red lights on the life support flashed green as the door to its airtight chamber unsealed and Shinji Ikari took his first real breath in what seemed like forever. His eyes slowly opened, and he was relieved to see not a white hospital roof, but a roof made of mirrors. The reflection greeting him was not what he expected. The time he had spent in the EVA had felt like an eternity, but he couldn't have known for sure. He closed his eyes as the time he spent in the EVA came flooding back, like a dream… or a nightmare.

_The first thing he noticed was the feeling of floating._

_Where am I?_

_The thought floated across his mind, as if he was hearing it instead of thinking it._

_The second thing he noticed was the sound. It was the piercing hum of total crushing silence; he felt the familiar icy grip of fear creep into his being, and fought against the urge to keep his eyes squeezed shut._

He opened his eyes again and stared at his reflection. His body had not matched the changes of his mind. He was looking at the exact same Shinji who had climbed into the EVA with the intention of saving Rei, the only change being his left eye. It was now a deep, shining red.

"The same color as blood," he thought.

He found the act of sitting up to be surprisingly easy. He couldn't have been unconscious for too long or his muscles would have complained quite a bit more. He took stock of his surroundings: he was sitting on what appeared to be NERV's standard automated ICU unit, and a small steel chair sat in the corner. The standard medical room was lit only by the sickly red glow given off by the ICU unit. He swung his legs over the edge of the bed and froze as he suddenly noticed a heavy metal weight around his neck. He looked up at the roof and his reflection revealed a black collar with a red inner ring.

"What the hell is this…?"

"_WHAT THE HELL IS GOING ON?!" he screamed again. His voice never echoed despite the vast feeling to the space he currently occupied. Panic had a firm grasp on his mind, and he frantically searched for something to prove that he wasn't going insane. _

"_IS THERE ANYONE THERE?" He wanted to cry, he wanted to curl into a ball and disappear, but nothing he tried worked. "I don't want to be alone…"_

"_Alone?"_

_He froze. A voice?_

_He turned towards the source and his panic was replaced by shock._

"_Mother?"_

He stood outside his small room, wearing what amounted to a very thin pair of pajamas, with his bare feet on the cold floor of the metallic hallway.

"Would it have killed them to leave me some shoes?" he mumbled.

His complaining stomach urged him into motion, and he set off in search of food and people; whichever he encountered first.

He continued down the hallway, following a string of cold white lights and a humming sound that seemed to come from everywhere. Was he on a ship? Maybe he could find a porthole or a ladder to the deck.

His thoughts were interrupted by footsteps from behind. He stopped and turned; he wouldn't see the person until they rounded the corner, and he would rather not be surprised.

An average-looking man with an average crew haircut wearing a standard tuxedo rounded the corner and stopped a standard ten feet from Shinji.

"I was wondering when one of you would show up," Shinji said. "Didn't happen to bring me something to eat, did you?"

The man didn't make any acknowledgement of the joke and stared at Shinji as he prepared to deliver his standard line.

"The commander wishes to see you," he said, no emotion in his voice. "You will follow me."

Shinji smiled to himself. He had missed it, no matter how standard it was.

"_You miss them?" she asked._

"_Yes," he replied. _

_It had been days, or weeks, or months since the image of his mother—Yui Ikari—had appeared, and he had no way of telling how much time had passed. He hated being trapped here, but at least he wasn't alone._

"_Why do you miss them?" she asked._

"_I don't know." He mumbled. "They hated me, used me, and all I can think about is how much I want to see them again."_

"_Used you?"_

_It had been this way since she had appeared: Evangelion Unit 01, in the guise of his mother. He had been happy beyond belief to see her, and for some reason he had felt only slight disappointment to learn that the EVA had only chosen his mother, the form it thought he would be most comfortable with, to appear to him as. And instead of providing him the comfort he so desperately craved, it asked questions. It wanted to know and learn about him, and since he was stuck here till someone got him out, he decided it couldn't hurt to answer its questions._

"_They only wanted me around because I could pilot the EVA, erm… pilot you." _

_He felt increasingly awkward referring to the EVA as an it, when it… she, sat right beside him._

"_And do you hate… piloting me?"_

_He hated the questions, but he hated the silence even more._

"_I don't know," he whimpered. "It just isn't fair."_

The agent led him through two more corridors identical to the first until he stopped and opened a heavy steel door.

"You will enter and sit in the chair," he stated, monotone.

"Sir, yes, sir," Shinji quipped, throwing a mocking salute.

He stepped through the door, into a perfectly square room. A single chair sat in the direct center, between him and a large reflective window that took up the top half of the opposite wall.

It reminded him of an interrogation room.

He stepped forward and sat in the chair, looking around for something interesting. He had spent a long time in a featureless abyss, and wasn't so keen on doing it again.

He didn't have to wait long before the glass wall shifted and became transparent, revealing a familiar face.

"Misato!" he cried. "You have no idea how glad I am to see you!"

He stood and walked towards the glass, now standing less than five feet from her, separated only by glass. He wanted to hug her, to tell her he was sorry, and that he loved her. But the expression on her face spawned a sinking feeling in his gut. He had expected relief, or annoyance at his happy attitude, but the look of contempt, loathing, _hatred_ on her face was not within his realm of expected reactions.

"What's wrong?" his happy attitude had evaporated. "What happened? Where are we?"

"_So where are we?" _

"_We are here."_

_He smiled; he had become used to her different point of view and had tried to adapt to her way of questioning._

"_Yes, but where is here?"_

_A rare—but slowly more often occurring—look of thoughtfulness crossed her face. He was getting better at this._

"_I… do not know."_

_That was a first._

"_Have you always been here?"_

"_Yes."_

_He felt no tiredness here, and as a result he had spent however long he had been here asking questions and being asked questions in return. He now felt she understood him better than anyone, and her questions had helped him understand himself. _

_They didn't hate him. They were afraid. He now realized that they didn't want him around not only because he was a pilot, but that they were just like him, afraid of being hurt, and because of that they all shut themselves in. With her help he had analyzed his memories over and over again, and every time it had become more obvious to him that he had been selfish and childish, and he had promised to be a different person when he got out of here… wherever here was._

"_Are we inside of you?" he was just shooting ideas at this point._

"_Yes."_

He turned back to his chair and sat down. His time inside the EVA had given him a much more logical and analytical mind, and he began piecing things together.

He was a prisoner.

It was the only explanation. The interrogation room, the guard that had most likely never been more than earshot away, and the metal collar around his neck.

He looked back at Misato with a serious expression the old Shinji never could have managed.

"What's going on?" he asked.

Misato's expression never changed, and she didn't reply.

"How long was I asleep?"

"Fourteen years."

The voice did not come from Misato, but from behind him. He turned to find a young brown-haired girl wearing a doctor's coat and carrying a clipboard.

"Fourteen years?!" he cried.

He had been trapped for a long time, but he had always estimated it to be about six months.

"We need to check your vitals. How are you feeling?"

He ignored her, no longer in the mood for any more questions.

"Where is Unit 01?" he asked, looking to Misato for an answer.

"You don't need to know that," she finally replied.

"Why not? I am the pilot, aren't I?"

Her expression grew even darker. "You are no longer anything, and you will never do anything again."

She turned and walked away from the glass, exiting through a door and leaving Shinji alone with the young doctor.

He turned back to her. "I'm confused, what's going on?"

She shook her head. "I'm sorry, I don't know the answer."

Shinji sighed as he walked towards the door.

"Wait!" the girl cried, grabbing his arm. "I need to know how you're feeling!"

He looked at her, emotions he hadn't felt in a long time bubbling to the surface.

"I'm sorry, I don't know the answer."

_He sat, floating in the abyss._

_He had long since run out of questions for the EVA, and they now floated in the crushing silence once again. _

_He had discovered that in his attempt to save Rei he had fused his mind with the EVA. They were now the same person, but… not the same person._

_He sighed. He didn't even want to try and make sense of it._

_The EVA had also revealed that his attempts to save Rei had been futile. He had saved her soul from the angel, but without a body her soul had dissipated and vanished._

_He no longer felt that he should have tried harder, or tried something else. He had given it his all and it hadn't been enough… but he would give more than his all next time._

The agent had led him to his cell and locked him in. The cell was an exact copy of the cell he been placed in when his former self had thrown a bit of a temper tantrum, with one small difference. His first cell hadn't had food in it.

He sat down on the metal bench and picked up the plastic tray. He ate slowly, savoring the taste of something he hadn't had in a long time. Fourteen years, apparently.

_He had gotten used to the silence and the feeling of floating in the featureless world, when it suddenly shuddered and began to crack. As cracks of light began to spread across his world he turned to where his constant companion always was. She had never left him in his time here, and he had become grateful for it._

"_What's happening?" he asked._

"_It is time for you to go," she replied._

_He felt sad; he had come to enjoy the presence of his mother, who was actually a giant cyborg. _

"_Thank you for being here. I'll never forget you."_

_She gave him a quizzical look. "We are the same person."_

"_We are now, but soon I'll be back in my own body."_

_She shook her head and smiled at him._

"_We are the same person."_

_He suddenly thought of more questions he wanted to ask, but the cracks blinded him with light and he lost consciousness._

The blaring red alarm lights blinded him as he sat up on the metal bench. He hadn't really slept, but it was easier to think when his eyes were closed. The standard agent stood in the doorway, his gun in his hand.

"Stand up," he growled.

Shinji complied. He no longer felt like making jokes.

"Follow me."

The agent led him down more of the boring metal corridors and into an elevator. Shinji was no stranger to tense elevator rides, and bore the event in silence.

The elevator doors opened up on the bridge of the ship and Shinji was greeted with the familiar sounds of battle preparation. Misato stood at the helm yelling orders to the crew, frantically preparing for some kind of launch.

Shinji stepped towards her. "Is it the angels?"

Misato glared at him. "No. It's the world you made."

A shockwave rocked the shape and Shinji looked out the windows at the fountain of red seawater a couple miles in front of the battle cruiser.

And from the water burst the last thing he had expected: Unit 00.

"Rei…" he breathed.

How was it possible? He had asked Unit 01 every question he could think of and every answer had led him to the same conclusion: Rei was dead.

He spun back to Misato. "Where is Unit 01!?"

She ignored him and turned to the agent. "Get him the hell out of here."

The agent grabbed his arm but he resisted, he wasn't finished yelling.

"Why won't you tell me what's going on!?" his frustration finally getting the better of him. "Why won't you let me help!"

Another explosion rocked the ship and he lost his footing, slamming into the wall and sliding to the floor.

Misato looked down on him. "You won't ever _help _again," she snarled, pulling a black remote from her pocket and brandishing it in his face. "And if you even get near an EVA again, that collar will kill you."

He finally understood. They hadn't brought him because they wanted his help. His actions had caused something horrible, and they'd pinned it all on him.

He felt rage force its way through his veins as he stood.

It wasn't fair.

He was okay with having made a mistake, even though he didn't know what it was. And he understood that they blamed him for it.

But he would not be their personal punching bag. Not again.

He opened his mouth, preparing to voice his rage, when the side of the bridge exploded inwards, throwing him back down to the ground. The hand of Unit 00 reached through the hole.

"Ikari!"

A voice he had never thought he would hear again reverberated through his skull, and shook him to the core. How was she still alive?

He brushed the debris from his clothes as he stood.

Misato had been knocked against the far wall and now stared at him from the floor.

"Don't!" she yelled, holding her thumb above the button on the remote. "Don't make me do it, Shinji!"

He felt the familiar feeling of fear creep up his spine. What should he do?

He could stay and be the object of their hate, or he could try to go and find the answers to his questions.

He looked at Misato and made his decision.

He took a step towards Unit 00.

"SHINJI!" Misato screamed.

Another step. He wouldn't let his fear control him again.

"Please don't make me do this!"

Another step. He would find the answers to his questions, and he would try the best he could to fix everything.

"GOD DAMN IT SHINJI, STOP!"

As he neared the EVA his left eye began to itch, and he realized there was a pressure in the back of his head. Had it been there the whole time?

"FUCK!" Misato cried as she slammed her thumb down on the button of the remote.

The collar around Shinji's neck separated into four pieces, spread out, and began to rotate two feet around him. The pieces gathered speed as Shinji looked towards Misato. She hated him, but there were tears running down her face.

He hadn't wanted things to go this way, but he couldn't change it now. He could only move forward.

The pieces gathered speed until they became a blur.

Why did his left eye itch so much?

The pieces stopped abruptly and shot straight towards his neck.

And half a foot from his neck each piece met with a wall of shining power.

Misato sat stunned as the AT fields pushed the pieces away from Shinji's neck, until the field that held them aloft died and they fell to the metal floor.

Shinji smiled to himself. "We are the same person."

He understood now.

When he'd fused with the EVA he had become something _more_. He and the EVA were now two pieces of the same being.

He still needed to find the answers to his questions, and he now had more of those than ever.

He placed his hand on the massive palm of Unit 00 and looked back towards Misato.

"I'm sorry."

He turned and climbed into the EVA's hand.

END


End file.
